Stop virus/trojan etc

Hi i was wondering if any one can help me. I had my site up and running for a couple of months and then last night i found out. that someone had put a trojan virus onto it. I was talking to the people who host my site and thier said "the scripting is out of date and has been hacked." This is becuase i ran my own anit vruis and their was no vruis on my pc. i was wondering if thier any way to stop this from happening?